From 904dafed30e4da63436e5303851c735a88ea1a4f Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 26 Mar 2019 11:39:12 +0000
Subject: [PATCH] JAL-3215 colours updated on help page

---
 help/html/colourSchemes/hydrophobic.html           |   42 ++++++++++----------
 src/jalview/schemes/ResidueProperties.java         |    2 +
 .../schemes/HydrophobicColourSchemeTest.java       |    1 -
 3 files changed, 23 insertions(+), 22 deletions(-)

diff --git a/help/html/colourSchemes/hydrophobic.html b/help/html/colourSchemes/hydrophobic.html
index 5caae8d..308f043 100755
--- a/help/html/colourSchemes/hydrophobic.html
+++ b/help/html/colourSchemes/hydrophobic.html
@@ -42,36 +42,36 @@ td {
     <table width="400" border="1">
       <tr>
         <td bgcolor="#ff0000">I</td>
-        <td bgcolor="#f60009">V</td>
-        <td bgcolor="#ea0015">L</td>
-        <td bgcolor="#cb0034">F</td>
-        <td bgcolor="#c2003d">C</td>
+        <td bgcolor="#f70009">V</td>
+        <td bgcolor="#eb0014">L</td>
+        <td bgcolor="#cf0030">F</td>
+        <td bgcolor="#c60039">C</td>
       </tr>
       <tr>
-        <td bgcolor="#b0004f">M</td>
-        <td bgcolor="#ad0052">A</td>
-        <td bgcolor="#6a0095">G</td>
-        <td bgcolor="#680097">X</td>
-        <td bgcolor="#61009e">T</td>
+        <td bgcolor="#b5004a">M</td>
+        <td bgcolor="#b3004c">A</td>
+        <td bgcolor="#74008b">G</td>
+        <td bgcolor="#72008d">X</td>
+        <td bgcolor="#6c0093">T</td>
       </tr>
       <tr>
-        <td bgcolor="#5e00a1">S</td>
-        <td bgcolor="#5b00a4">W</td>
-        <td bgcolor="#4f00b0">Y</td>
-        <td bgcolor="#4600b9">P</td>
-        <td bgcolor="#1500ea">H</td>
+        <td bgcolor="#690096">S</td>
+        <td bgcolor="#660099">W</td>
+        <td bgcolor="#5b00a4">Y</td>
+        <td bgcolor="#5200ad">P</td>
+        <td bgcolor="#2500da">H</td>
       </tr>
       <tr>
-        <td bgcolor="#0c00f3">E</td>
-        <td bgcolor="#0c00f3">Z</td>
-        <td bgcolor="#0c00f3">Q</td>
-        <td bgcolor="#0c00f3">D</td>
-        <td bgcolor="#0c00f3">B</td>
+        <td bgcolor="#1c00e3">E</td>
+        <td bgcolor="#1c00e3">Z</td>
+        <td bgcolor="#1c00e3">Q</td>
+        <td bgcolor="#1c00e3">D</td>
+        <td bgcolor="#1c00e3">B</td>
       </tr>
       <tr>
         </td>
-        <td bgcolor="#0c00f3">N</td>
-        <td bgcolor="#0000ff">K</td>
+        <td bgcolor="#1c00e3">N</td>
+        <td bgcolor="#1100ee">K</td>
         <td bgcolor="#0000ff">R</td>
       </tr>
     </table>
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index fb5d5a8..68c9098 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -406,6 +406,7 @@ public class ResidueProperties
   };
 
   // Dunno where I got these numbers from
+  /*
   public static final double[] hyd2 = { 0.62, // A
       0.29, // R
       -0.90, // N
@@ -430,6 +431,7 @@ public class ResidueProperties
       0.0, // Z
       0.0 // X
   };
+  */
 
   public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11,
       1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83,
diff --git a/test/jalview/schemes/HydrophobicColourSchemeTest.java b/test/jalview/schemes/HydrophobicColourSchemeTest.java
index a0a2281..3ca1780 100644
--- a/test/jalview/schemes/HydrophobicColourSchemeTest.java
+++ b/test/jalview/schemes/HydrophobicColourSchemeTest.java
@@ -55,7 +55,6 @@ public class HydrophobicColourSchemeTest
     assertEquals(scheme.findColour('z', 0, null), new Color(28, 0, 227));
     assertEquals(scheme.findColour('x', 0, null), new Color(114, 0, 141));
     assertEquals(scheme.findColour('?', 0, null), new Color(128, 0, 128));
-    assertEquals(scheme.findColour('?', 0, null), new Color(128, 0, 128));
   }
 
 }
-- 
1.7.10.2